Our vote for the best pizza in San Francisco is at Caffe BaoNecci in North Beach (Green & Columbus). This is a small family-run restaurant (they're from Lucca) that serves delicious (very) thin-crust pizza. I asked if they would make us a plain crust, brush it with olive oil, salt it and serve in pieces. I've had this many times in Montecatini (near Lucca) and have craved it often, and BaoNecci's was made to a 'T'. Bill thinks the eggplant parmesan here is delicious as well.
http://www.caffebaonecci.com/caffebaonecci/Welcome.html
Rose's Cafe on Union Street (Cow Hollow) also has delicious thin-crust pizza, and they too made the plain oiled and salted crust for us, which was almost as good as BaoNecci - Rose's crust just slightly thicker but still very thin. Rose's Cafe is very a popular restaurant.
http://www.rosescafesf.com/
We also had pizza at Tony's Pizza Napoletana in North Beach (Union & Stockton) which we liked, a little thicker pizza that we're used too, also a very popular restaurant and always crowded.
http://www.tonyspizzanapoletana.com/
We have yet to go back to Tomasso's in North Beach which we ate at a few years ago, and to A16 on Chestnut Street in the Marina, which was recommended to us.
http://tommasos.com/
http://www.a16sf.com/
These are just pizza restaurants; we have other Italian favorites, too, which I'll write about soon.